1. Field of the Invention
The invention relates to the fields of nucleic acid polymerases and nucleic acid polymerization reactions.
2. Introduction
The efficiency of a nucleic acid polymerization reaction has implications for numerous assays and techniques. For example, the ability to enhance polymerase activity in a PCR process increases the sensitivity of the PCR-based assay. We have identified, produced, purified, and analyzed novel extracts, proteins, and complexes that improve the polymerization activity of nucleic acid polymerases. Included within the aspects of the present invention are methods for identifying compositions with a polymerase enhancing activity, methods for purifying and using these compositions, and specific extracts, proteins, and complexes that function to enhance polymerase activity.
3. Description of Related Art
Manipulating nucleic acids with polymerization reactions is a fundamental component of biotechnology-related research. These reactions permit researchers to replicate DNA or RNA in vitro, which in turn allows cloning or amplification of specific nucleic acids or groups of nucleic acids. Numerous other examples exist detailing the critical nature of a nucleic acid polymerization reaction or a nucleic acid polymerization enzyme in a particular technique, including sequencing nucleic adds, mutagenesis of nucleic acid sequences, and producing nucleic acid probes for hybridization. Of particular current interest are amplification reactions, such as PCR, that have greatly increased the rate at which researchers can perform nucleic acid related experimentation. Extremely rare nucleic acids can now be amplified and manipulated using these techniques, which necessarily involve nucleic acid polymerases.
Using techniques with an amplification step has driven concern for the efficiency, fidelity, and sensitivity of the polymerase used. This has resulted in efforts to both analyze and optimize polymerization conditions for a variety of applications. (Lundberg et al., Gene 108: 1-6 (1991); Eckert and Kunkel, PCR Methods Applic. 1: 17-24 (1991); Ling et al., PCR Methods Applic. 1: 63-69 (1991); Brail et al., Mutat. Res. 303: 75-82 (1994); Garrity and Wold, P.N.A.S. 89: 1021-1025 (1992); Taylor and Logan, Curr. Opin. Biotechnol. 6: 24-29 (1995)) In particular, quantitative amplification-based reactions rely upon the ability to efficiently amplify each nucleic acid species present in a sample. (See Ausubel, et al., Chapter 15, In: Current Protocols in Molecular Biology, John Wiley and Sons (1992) and supplements through 1995.) Thus, both a concern for the accuracy of and a need for new methods to enhance the performance of amplification-based nucleic acid techniques exists in the art.
One way in which these concerns and needs have been addressed is through the use of additives to the amplification reaction. Different additives act at different points in the amplification process. For example, formamide has been used to increase the specificity of PCR with GC rich target sequences, which are particularly susceptible to intramolecular hybridization that may prevent hybridization with a primer. (Sarkar, G. et al. Nucl. Acids Res. 18: 7465 (1990)). It has also been reported that tetramethylammonium chloride increases yield and specificity of PCR reactions. (Chevet, E., et. al., Nucleic Acids Res. 23:3343-3334 (1995).) Hung et al. report the reduction in multiple satellite bands from amplifying complex DNA when dimethyl sulfoxide (DMSO) is added. (Hung, T., et al. Nucl. Acids Res. 18: 4953(1990).) The multiple satellite bands often present problems in purifying the desired amplification product from the other DNA present.
Certain proteins have been used to stabilize hybridized nucleic acids during replication. For example, E. coli single-stranded. DNA binding protein has been used to increase the yield and specificity of primer extension reactions and PCR reactions. (U.S. Pat. Nos. 5,449,603 and 5,534,407.) The gene 32 protein (single stranded DNA binding protein) of phage T4 apparently improves the ability to amplify larger DNA fragments (Schwartz, et al., Nucl. Acids Res. 18: 1079 (1990)) and enhances DNA polymerase fidelity (Huang, DNA Cell. Biol. 15: 589-594 (1996)). In addition, bacterial thioredoxin combined with T7 DNA polymerase (Sequenase(trademark); Amersham-USB) has been used to increase processivity, but the combination is not active at high temperatures, such as those used in PCR.
Another way amplification-based assays and techniques have been improved is through the development of modified polymerases or the use of combinations of polymerases. (U.S. Pat. No. 5,566,772) For example, the TaKaRa long PCR kit employs two polymerases (Takara Shuzo Co., Ltd; Japan), and a number of polymerase combinations were also tested by Bames (Proc. Nat. Acad. Sci. USA, 91:2216-2220 (1994). Truncated Taq and T. flavus DNA polymerase A enzymes that apparently exhibit increased thermostability and fidelity in PCR have also been suggested. (U.S. Pat. No. 5,436,149.) Combinations of polymerases with and without 5xe2x80x2-3xe2x80x2 exonuclease or 3xe2x80x2-5xe2x80x2 proofreading activity have also been used. (U.S. Pat. No. 5,489,523)
Further, amplification-based assays and techniques have been improved through empirical testing of conditions, reagents, and reagent concentrations to optimize polymerization reactions with a particular enzyme. Temperature and length of amplification cycles, primer length, and pH, for example, are all conditions that can be optimized. (Bames, Proc. Nat. Acad. Sci. USA, 91:2216-2220 (1994).)
However, accessory proteins can be even more useful in improving polymerase activity and/or the processivity of polymerases. xe2x80x9cProcessivityxe2x80x9d in this context refers to the number of enzymatic reactions occurring each time an enzyme binds to its substrate. In the context of nucleic acid replication reactions, xe2x80x9cprocessivityxe2x80x9d means the number of bases that can be replicated when the polymerase binds to a priming site. An increase in processivity directly relates to longer replication products.
Intracellular replication has been shown to involve accessory proteins, as characterized in E. coli, human, and phage T4 systems. The accessory proteins interact with polymerases to improve activity and provide the high processivity necessary to replicate genomic DNA efficiently while avoiding unacceptable mutation rates. Since the accessory proteins can be used in combination with the other improvements noted above, the development and application of accessory proteins holds particular promise for enhancing the results of nucleic acid replication-based reactions.
Accessory proteins have been identified in eukaryotes, E. coli, and bacteriophage-T4 and are thought to form xe2x80x9csliding clampxe2x80x9d structures. (Kelman and O""Donnell, Nucl. Acids. Res. 23(18): 3613-3620 (1995).) These structures are thought to tether the polymerase to DNA, thereby increasing processivity. The sliding clamp structures, however, have largely been studied in in vitro model systems. Only in the case of T4 polymerase has knowledge of the activity of such accessory proteins been used to improve polymerization-based techniques employed by researchers in the art. For example, accessory proteins of the T4 holoenzyme have been reported to improve processivity when added to polymerization systems using T4 polymerase. (Young et al., Biochem. 31(37): 8675-8690 (1992); Oncor Fidelity(trademark) Sequencing System, Oncor; Gaithersburg, Md.) However, since the T4 accessory proteins are derived from bacteriophage, they are not likely to enhance polymerases from bacteria, archae, or eukaryotes. Thus, the use of T4 accessory proteins is believed to have been limited to techniques where T4 polymerase is used.
The presence of dUTP (deoxyuracil triphosphate) in a polymerization reaction and the effect of deoxyuridine-containing DNA on DNA synthesis have also been examined. In particular, deoxyuridine in a DNA strand has been shown to inhibit polymerization by archael DNA polymerases. (Lasken, et al., (1996) J. Biol. Chem. 271; 17692-17696.) While Lasken et al. reported that archeal DNA polymerases, such as Vent, are inhibited by DNA containing deoxyuridine, they do not discuss the effect of removing uracil-containing nucleosides or nucleoside triphosphates from the reaction to prevent incorporation. Furthermore, they do not discuss any enzyme that acts on or turns over dUTP in a reaction. Neither do they mention any dUTPase activity or the possible effect of dUTPase activity on polymerization reactions. In addition, Lasken et al. do not appreciate the fact that dUTP is generated during the course of a normal PCR reaction by the deamination of dCTP. As a result of the deamination, dUTP will be present and be incorporated into an amplified nucleic acid, inhibiting the polymerase activity. Thus, the art has not appreciated the potential of dUTPase activities and proteins in enhancing replication reactions.
Accordingly, since present knowledge and use of accessory proteins has led to limited applications in replication-based techniques, there continues to exist a need in the art for new and more widely useful compositions for enhancing polymerase enzyme activity. The present invention meets this need.
The present invention comprises extracts, protein complexes, and related proteins that possess nucleic acid polymerase enhancing activity useful in a variety of replication reactions known in the art. Thus, the extracts, protein complexes, and related proteins of the invention function to enhance a wide spectrum of in vitro nucleic acid replication reactions by providing, inter alia, replication products of superior length, fidelity or both, and at higher yields. As used in this specification and appended claims xe2x80x9cpolymerase enhancing activityxe2x80x9d means the ability to increase the rate, fidelity, and/or yield of a nucleic acid polymerization reaction mediated by a nucleic acid polymerase, or to expand or alter the range of conditions under which such reaction does or may proceed.
In one aspect of the invention, extracts of Pyrococcus furiosus (Pfu) cells are provided that enhance the activity of Pfu DNA polymerase. The extracts enhance nucleic acid replication product yields over a fairly broad range of concentrations and contain at least one polymerase enhancing factor. As used in this specification and in the appended claims, the term xe2x80x9cPEFxe2x80x9d includes purified naturally occurring polymerase enhancing factors and wholly or partially synthetic copies or active analogs thereof. In accordance with the invention, such extracts can be further purified by heparin affinity chromatography followed by sepharose gel purification. Additionally, PEFs can be identified and purified using the antibodies of this invention, discussed below. While Pfu cell samples were used and are specifically exemplified below, one skilled in the art will appreciate that other cell samples can be used to identify and purify PEFs. For example, other species of the archae Pyrococcus or Thermococcus can be used as well as thermophilic bacteria cells and other bacteria cells. In addition, eukaryotic cells and tissues can be used as a source for PEF, as demonstrated by the cloning and expression of human dUTPase, which also enhances polymerase activity, Thus, the invention also comprises compositions and methods wherein a dUTPase or any activity that turns-over dUTP is capable of acting to enhance a nucleic acid polymerization reaction.
In another aspect of the invention, PEF complexes are provided. The PEF complexes of the invention possess polymerase enhancing activity and generally comprise multiple protein subunits with a combined molecular weight of approximately 250 kD or above as determined by SDS-PAGE analysis and gel filtration of unheated PEF samples. An example of one PEF complex (P300) was purified from Pfu cell sample extracts. The predominant components of the complex are a 50 kD protein (P50) and a 45 kD protein (P45). Heat treating the Pfu P45 with 2% SDS and 1% TCA produces a 17-18 kD protein, which represents the fully denatured form. However, the Pfu PEF complex contains other minor components with approximate apparent molecular weights of 150, 100, 85, 60, 55, 42, and 37 kD. At least two components (150 and 100) have been shown to be dimeric or polymeric forms of P50. Thus, the PEF complexes of the invention comprise protein components and function to enhance the activity of polymerases.
In another aspect of the invention, Pfu proteins possessing polymerase enhancing activity are provided. These proteins have molecular weights between approximately 42 and 60 kD by SDS PAGE analysis under partially denaturing conditions. The 42-60 kD proteins may be used alone or in combination to enhance polymerase activity. Methods for purifying these proteins as well as the PEF extracts and PEF complexes from which they have been isolated are also provided.
The invention also involves two particular proteins, Pfu P50 and P45, which are predominant components of the PEF complex (P300). Detailed structural and functional information on the Pfu P45 and P50 proteins is disclosed. The P50 protein is similar in structure to a bacterial flavoprotein. The P45 protein is similar in structure to dCTP deaminase, functions as a dUTPase, and possesses polymerase enhancing activity. The structural information herein can be used to generate specific hybridization probes that detect the presence of nucleic acids encoding a protein that is part of a PEF complex, or related proteins from samples from other species, or possesses PEF activity. Furthermore, the structural information can be used to generate proteins from expression systems known in the art, synthetic proteins, partially synthetic proteins, or proteins made from a combination of natural proteins, expressed proteins, and synthetic proteins. Methods for detecting the presence or absence of polymerase enhancing activity and/or dUTPase activity are also included in this invention and can be used to identify the various active PEF proteins or analogs. In addition, polyclonal or monoclonal antibodies that bind to PEF components can be produced, for example from purified P45 or P50, purified PEF complexes (P300), or another PEF of the invention. These antibodies can then be employed in assays and kits, well known in the art, in order to identify the presence or absence of a PEF.
The understanding of the catalytic activity of PEF, and the P45 protein in particular, provides aspects of this invention directed to polymerase enhancing proteins, as well as methods, kits, and compositions containing a dUTPase activity or dUTPase protein as a PEF. Thus, a dUTPase activity or dUTPase protein or composition can be used to enhance nucleic acid replication, polymerization, or PCR reactions according to this invention. In fact, any activity that functions to turn-over dUTP can be used as a polymerase enhancing activity of this invention. Wide-ranging sources for the dUTPase activity, protein, or composition exist, as it is demonstrated to be present from both archael and human sources, the ends of the phytogenetic possibilities. Thus, any cell or species can be used as a source for polymerase enhancing activity or PEF.
Kits for replicating nucleic acids and methods for using the PEF complexes, specific proteins of the complexes, and extracts containing PEF are also provided. In addition, the complexes, proteins, and extracts can be used in compositions comprising a polymerase. Ideally, the polymerase will be one that is enhanced by the complex, protein, or PEF. The PEF extracts, complexes and proteins of the present invention are particularly useful in mixtures with nucleic acid polymerases, such as native polymerases, those produced by recombinant DNA techniques, and kits containing such polymerases.
Also provided in the invention are methods for identifying proteins or complexes that influence nucleic acid polymerases. The source of the protein can be any bacterial, archael, or eukaryotic species. Certain embodiments involve methods for identifying proteins affecting polymerases used in amplification reactions, for example, alpha-type DNA polymerases such as DNA polymerases from Pyrococcus and Thermophilis species. Other embodiments involve the analysis of dUTPase activity as well as computer implemented screening methods to identify a PEF.